For 1 year. If he's a 4 WAR player out of the gate, he'll be a super 2 and be arb eligible for the 2017 season. If that's the case, he won't be making 500k at that point, and will certainly be making more than Pedroia by his third year of arb eligibility. So while, yes, up front Betts has a chance to exceed his paycheck by a huge amount, that gap will dwindle a bit each year he continues to be that good and the scales could very well tip the other way in years 5 and 6 of the control they have over him.
Granted, it's just as possible that Pedroia's on the field value declines over the same span, but it's not like they have an eternally renewing option for Betts at 500k per season. If we use 7 million per win and assume Mookie is worth 28 million a year every one of the next six years, he's worth 168 million. If he's paid 500k in the next two years and then hits arb at like 2 million, and escalates to 10, 15 and 20 from there, he'll be paid 46 million giving him an excess value of 122 million. If Pedroia is a 5 win player for the next 6 years, he's worth 210 million in that span and will be paid 85.25 million. That's an excess value of 127.75 million.
These numbers aren't meant to be exact. I'm just illustrating a point. Obviously both players have a range of possibilities ahead of them, but it's no given that Betts will provide more excess value in the next 6 years.